BMI503: Biomedical Informatics Systems, Databases and Software Methods

Course Information

Instructor

Dr. Jaroslaw Zola

Department of Computer Science and Engineering
Department of Biomedical Informatics

Email: jzola@buffalo.edu
Web: http://www.jzola.org/
Twitter: @rzolau

Course Description

This course provides Biomedical Informatics graduate students and clinical fellows with a technical overview of the current computing and information technology systems, programming languages and software development tools available to manage, access and analyze health and biomedical data. The systems are presented in the context of effective patient care as well as research settings.

Course Organization

The course consists of a series of lectures complemented by a practical demonstrations and exercises. The course outline is provided below. Note that the course content is usually adjusted to meet students' requests, and hence it may sometimes diverge from what is below.

Student Learning Outcomes

Upon completion of the course you will gain:

Course Requirements

The course has three requirements:

  1. Class attendance and participation in in-class discussions You will be expected to read assigned material, for example journal papers, and actively engage in discussion with instructor and other students.
  2. Laboratory exercises Each course section will be complemented with graded hands-on practical exercises testing practical aspects of the covered material.
  3. Final exam The course will be concluded with open books/open notes final exam testing your knowledge from all covered topics.

Grading Policy

The final grade will be weighted average: 10% class attendance and participation, 45% laboratory exercises, 45% final exam. The number-to-letter grade mapping will be done as indicated in the table below:

Score Grade Points
90-100 A 4.0
85-89 A- 3.67
80-84 B+ 3.33
75-79 B 3.0
70-74 B- 2.67
65-69 C+ 2.33
60-64 C 2.00
55-59 C- 1.67
50-54 D 1
0-49 F 0.0

In general, no incomplete grades (IU or I) will be given. However, in special circumstances that are truly beyond your control and justify incomplete grade, we will follow the university policy on incomplete grades, available here.

Course Materials

This course does not rely on one specific textbook. However, the following book is suggested (but not required) as a complement to the lectures' content:

Additionally, several research papers may be referenced during the course.

Computing Resources

For the duration of the course you will be granted access to the resources (including storage) provided by the UB Center for Computational Research (CCR). CCR is the state-of-the-art HPC and data center hosting clusters, multi-core compute nodes, and compute nodes with GPGPU accelerators. It provides programming and execution environments supporting all types of parallelism covered in this course. Additionally, a virtual environment with a Linux distribution and all required compilers and runtime systems will be available for offline use.

Academic Integrity

You must be familiar with the university policies on academic integrity!!! The university policies for graduate students are available here.

Any violation of these policies, including but not limited to cheating on any course deliverable (e.g., homework project, exam, etc.), will result in automatic failure of the course.

Accessibility Resources

If you have any disability that requires reasonable accommodations to enable you to participate in this course, please contact the Office of Accessibility Resources, 25 Capen Hall, Phone: (716) 645-2608, and also the instructor of this course. The office will provide you with information and review appropriate arrangements for reasonable accommodations. In case you require accommodations, you must inform your instructor at the beginning of the course!